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As far as the ideals of world who believes whole-heartedly in the separation of church and state would believe, the answer should be a resounding "yes". However, personally I would be hesitant to put that burden on them.
And if you think of the separation of church and state as being complete for either side, not paying taxes may be a distinct representation of such separation.

After all, if churches begin to pay taxes, they will have a legitimate claim to a voice within the government. As an atheist, I would be much happier to see a bad church fade away from a community as it becomes further and further irrelevant rather than a vocal minority who maintains its beliefs within government body.

After all, if churches begin to pay taxes, they will have a legitimate claim to a voice within the government.

Paying taxes wouldn't give the church any stronger voice in the government then they do now. Their patrons and priests already can vote as they are citizens and can use their votes to affect the government. Also technically a church since it is tax free is not allowed to tell their patrons what to do political. But they already ignore this with protests about abortion, priests telling their patrons who to vote for and etc. They should lose their tax exempt for this but the IRS doesn't do jack shit about it.

Paying taxes wouldn't give the church any stronger voice in the government then they do now

Yes, actually, it would. religious protests and voting based on religious preference have no base in law, they are just the voice of a community who desire the world to function in a specific way. It's just the way people think, and they act accordingly. Nobody had to vote for a senator who happens to be a fundamentalist, but they did because the democratic community firmly believes (however unfounded) that such a senator has the best interest of the constitution in mind.

Tax them, and they have a right to know what the government is doing with their money. If you think they're vocal now, wait till you help yourself to their cash.

Maybe because I live in Canada I find the issue of tax-free churches to be much smaller, as we don't have as many mega churches as the states, or as many religiously motivated politicians. But I do know that religion is phasing itself out. Our generation is becoming more and more atheist, and we should rely not on trying to push out religion, but replacing it. Canada is further ahead in that sense, and hopefully the states aren't that far behind.

Tax them, and they have a right to know what the government is doing with their money.

Taxing them doesn't change their ability to affect law though. They get no new legal recourse because they pay taxes. As a business owner there is nothing I get to see or do that a church doesn't because I pay property taxes and they don't. They would still need to vote and to gather their constituents to their cause which they currently do now. They already have lobbyist and pay money to get laws passed in their favor. A perfect example is how last month North Carolina tried to pass a law making Christianity the official religion of the state. How much more vocal and entrenched could they get?

Maybe because I live in Canada I find the issue of tax-free churches to be much smaller, as we don't have as many mega churches as the states, or as many religiously motivated politicians.